Visualizing Satellite-Measured Optical Properties and Pigments in IDV: Giovanni

9.18 Visualizing Satellite-Measured Optical Properties and Pigments in IDV: Giovanni

Exercise Title: Visualizing Satellite-Measured Optical Properties and Pigments in IDV: Giovanni
Abstract: In this exercise you'll learn how to find and download chlorophyll and/or optical properties from the MODIS Aqua satellite, published in NetCDF format through the relatively new Giovanni data server at US NASA. The products are delayed up to 8 days by the aggregation process, but this is usually acceptable for optical properties (except sudden phytoplankton blooms; see the parallel Ocean Color Web exercise in such cases). The strength of this exercise is that it provides digital data that can be manipulated in MDL viewing software, thus allowing desirable value range manipulations not easily possible with the Ocean Color Web products. A new method for Saga display is added at the end for your interest.
Preliminary Reading (in OceanTeacher, unless otherwise indicated):
- Remote Sensing Data Concepts
- Marine Parameters from Remote Sensors
Required Software:
- IDV
- Saga
Other Resources:
- Integrated Data Viewer (IDV) Preliminary Setup
- Optical Oceanography - Niels Jerlov's seminal book
- Giovanni - NASA data server that "provides a simple and intuitive way to visualize, analyze, and access vast amounts of Earth science remote sensing data without having to download the data." [from the website]
- South Equatorial System Current - Article in the CIMAS Current Atlas
- US NASA Day of Year Calendar
Author: Murray Brown
Version: May 2013

1. Open the Giovannia main page, and spend a little time reading about it.

2. In the set of horizontal menu tabs, find and select OCEAN PORTALS.

Find and select OCEAN COLOR RADIOMETRY 8-DAY DATA.

3. This opens a nice graphical interface with a global map.

4. Below the map, enter the coordinates of your area of interest. Then click UPDATE MAP.

5. Check to make sure this updated map covers the area you really want. Make changes if necessary.

6. Find and check the item CHLOROPHYLL A CONCENTRATION 4KM, 8-DAY

7. Look lower to read about the time selection controls. You must enter dates that exactly match the 8-day averaging periods of the Giovanni system. And you cannot request anything later than the DATE END given there.

8. There is a link just below to a CALENDAR of 8-DAY INTERVALS. Open it, and find the latest interval that meets the Giovanni rules. It is shown here in bold red.

Just pick an exact interval, as stated here. Other dates give strange results.

Calendar of 8-day Intervals [from NASA website]

8-day Index	Non-leap Year Begin - End Dates	Leap Year Begin - End Dates
1	Jan 01 - Jan 08	Jan 01 - Jan 08
2	Jan 09 - Jan 16	Jan 09 - Jan 16
3	Jan 17 - Jan 24	Jan 17 - Jan 24
4	Jan 25 - Feb 01	Jan 25 - Feb 01
5	Feb 02 - Feb 09	Feb 02 - Feb 09
6	Feb 10 - Feb 17	Feb 10 - Feb 17
7	Feb 18 - Feb 25	Feb 18 - Feb 25
8	Feb 26 - Mar 05	Feb 26 - Feb 04
9	Mar 06 - Mar 13	Feb 05 - Mar 12
10	Mar 14 - Mar 21	Mar 13 - Mar 20
11	Mar 22 - Mar 29	Mar 21 - Mar 28
12	Mar 30 - Apr 06	Mar 29 - Apr 05
13	Apr 07 - Apr 14	Apr 06 - Apr 13
14	Apr 15 - Apr 22	Apr 14 - Apr 21
15	Apr 23 - Apr 30	Apr 22 - Apr 29
16	May 01 - May 08	Apr 30 - May 07
17	May 09 - May 16	May 08 - May 15
18	May 17 - May 24	May 16 - May 23
19	May 25 - Jun 01	May 24 - May 31
20	Jun 02 - Jun 09	Jun 01 - Jun 08
21	Jun 10 - Jun 17	Jun 09 - Jun 16
22	Jun 18 - Jun 25	Jun 17 - Jun 24
23	Jun 26 - Jul 03	Jun 25 - Jul 02
24	Jul 04 - Jul 11	Jul 03 - Jul 10
25	Jul 12 - Jul 19	Jul 11 - Jul 18
26	Jul 20 - Jul 27	Jul 19 - Jul 26
27	Jul 28 - Aug 04	Jul 27 - Aug 03
28	Aug 05 - Aug 12	Aug 04 - Aug 11
29	Aug 13 - Aug 20	Aug 12 - Aug 19
30	Aug 21 - Aug 28	Aug 20 - Aug 27
31	Aug 29 - Sep 05	Aug 28 - Sep 04
32	Sep 06 - Sep 13	Sep 05 - Sep 12
33	Sep 14 - Sep 21	Sep 13 - Sep 20
34	Sep 22 - Sep 29	Sep 21 - Sep 28
35	Sep 30 - Oct 07	Sep 29 - Oct 06
36	Oct 08 - Oct 15	Oct 07 - Oct 14
37	Oct 16 - Oct 23	Oct 15 - Oct 22
38	Oct 24 - Oct 31	Oct 23 - Oct 30
39	Nov 01 - Nov 08	Oct 31 - Nov 07
40	Nov 09 - Nov 16	Nov 08 - Nov 15
41	Nov 17 - Nov 24	Nov 16 - Nov 23
42	Nov 25 - Dec 02	Nov 24 - Dec 01
43	Dec 03 - Dec 10	Dec 02 - Dec 09
44	Dec 11- Dec 18	Dec 10 - Dec 17
45	Dec 19 - Dec 26	Dec 18 - Dec 25
46	Dec 27 - Dec 31	Dec 26 - Dec 31

9. This lesson was written in a Leap Year, so here are the values entered by the author.

10. Click EDIT PREFERENCES, to see these controls:

Set DECORATION FLAG to NO
Set SMOOTH FLAG to NO
Set CHLOROPHYLL PARAMETER MIN to 0.00, the value often suggested by NASA in HDF metadata
Set CHLOROPHYLL PARAMETER MAX to 64, similarly suggested by NASA; you can use a lower value later for better visual results

Then click GENERATE VISUALIZATION.

11. The process may require a number of "Click here to allow new window to open" controls. Just keep it moving.

12. Finally, here is the chlorophyll image. Notice an East-West band of slightly higher chlorophyll in the open sea, and the usual high levels along the coast.

13. Click on DOWNLOAD DATA

14. You'll see this wide control panel. The top level, INITIAL DATA RETRIEVAL refers to the entire global dataset, which we want to avoid. The bottom level refers to the TWO DIMENSIONAL MAP PLOT, which is Giovanni's odd way of saying "data subset".

15. To the right of the TWO DIMENSIONAL MAP PLOT, put a check beside NCD (you can also check KMZ if you want to see the image in Google Earth).

Then click on the lower DOWNLOAD IN BATCH control.

16. Finally this link appears, with your file. Notice that it is not very big; a much larger file might indicate you requested the globe and not the subset.

17. Download the GZ file to the folder LIBERIA > DATA > OCEAN > GIOVANNI with the same filename. Then unzip it in place to yield a datafile with the name A20121292012136.L3m_8D_CHL_chlor_a_4km.G3.gridSubsetter.nc, or similar. Notice that the dates (begin and end) consist of YYYYddd, where YYYY is the year, and ddd is the year day. Use the Day of Year calendar, above, to translate these values.

18. Run IDV.

19. On the dashboard, use DATA CHOOSERS > FILES to locate and open the new NC file with ADD SOURCE.

20. After it is loaded, select it in FIELDS, and then in DISPLAYS select COLOR-SHADED PLAN VIEW.

Then click CREATE DISPLAY.

21. Here is the initial plot. Notice that the chlorophyll features don't show up. We need to adjust the palette to see them.

22. On the dashboard, use the DISPLAYS tab to see these controls.

Here we've already used COLOR TABLE > RADAR > DBZ to select a rainbow palette. Click on the same control to CHANGE RANGE.

Change the values to 0.0 to 1.0 to emphasize very low values. Apparently IDV does not have a logarithmic display mode.

23. And now you can see the chlorophyll large-scale structure. The East-West band is possibly associated with the core of the South Equatorial System Current (see the article linked above).

24. To save this analysis, use FILE > SAVE AS and navigate to the folder PRODUCTS > IDV and save it with the filename A20121292012136.L3m_8D_CHL_chlor_a_4km.G3.gridSubsetter.nc.xidv

25. In addition to display in IDV, we've found that Giovanni NetCDF grids are well-formed, and can be used in Saga. Here's an example, using the grid above.

26. In Saga select MODULES > IMPORT/EXPORT-GDAL/OGR > Import Raster. Select the Same file as Panel 23, and use these settings. Then click OK.

NOTE: Experiments with Giovanni NetCDF grids show that TRANSFORMATION is needed to obtain a geographic referencing system.

27. Here is the grid in a Saga map, with a rainbow color palette, viewed in LOG MODE with a stretch factor of 1000.

28. So we have the infinite flexibility of IDV for display of the Giovanni data, plus the publication-ready graphics of Saga, if desired.

9.18 Visualizing Satellite-Measured Optical Properties and Pigments in IDV: Giovanni